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- PDB-3nef: High-resolution pyrabactin-bound PYL1 structure -

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Basic information

Entry
Database: PDB / ID: 3nef
TitleHigh-resolution pyrabactin-bound PYL1 structure
ComponentsAbscisic acid receptor PYL1
KeywordsHYDROLASE / PYL1 / Pyrabactin / HORMONE RECEPTOR
Function / homology
Function and homology information


regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / plastid / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding ...regulation of protein serine/threonine phosphatase activity / protein phosphatase inhibitor complex / abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / plastid / defense response / signaling receptor activity / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PYV / Abscisic acid receptor PYL1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYan, N.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Functional mechanism of the ABA agonist pyrabactin
Authors: Hao, Q. / Yin, P. / Yan, C. / Yuan, X. / Li, W. / Zhang, Z. / Liu, L. / Wang, J. / Yan, N.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Abscisic acid receptor PYL1
B: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0333
Polymers46,6562
Non-polymers3771
Water2,216123
1
A: Abscisic acid receptor PYL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7052
Polymers23,3281
Non-polymers3771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Abscisic acid receptor PYL1


Theoretical massNumber of molelcules
Total (without water)23,3281
Polymers23,3281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.57, 128.57, 87.24
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Abscisic acid receptor PYL1 / PYL1 / PYR1-like protein 1 / ABI1-binding protein 6 / Regulatory components of ABA receptor 9


Mass: 23327.898 Da / Num. of mol.: 2 / Fragment: UNP residues 20-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8VZS8, protein-serine/threonine phosphatase
#2: Chemical ChemComp-PYV / 4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide / Pyrabactin


Mass: 377.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13BrN2O2S / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.46 Å3/Da / Density % sol: 72.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M citric acid pH 5.5, 0.01M GSH/GSSG, 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9067 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9067 Å / Relative weight: 1
ReflectionResolution: 2.4→40.616 Å / Num. all: 30549 / Num. obs: 30549 / % possible obs: 92.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.6 / % possible all: 54.8

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KDJ

3kdj


Resolution: 2.4→40.616 Å / Occupancy max: 1 / Occupancy min: 0.94 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2228 1639 5.37 %
Rwork0.1881 28910 -
obs0.1899 30549 92.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.094 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 149.72 Å2 / Biso mean: 56.312 Å2 / Biso min: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1-6.985 Å2-0 Å2-0 Å2
2--6.985 Å20 Å2
3----13.9699 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2870 0 22 123 3015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082943
X-RAY DIFFRACTIONf_angle_d1.1423988
X-RAY DIFFRACTIONf_dihedral_angle_d17.8181076
X-RAY DIFFRACTIONf_chiral_restr0.078453
X-RAY DIFFRACTIONf_plane_restr0.004520
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47070.2711290.24651160X-RAY DIFFRACTION47
2.4707-2.5504000.24461911X-RAY DIFFRACTION71
2.5504-2.64150.29682900.25962386X-RAY DIFFRACTION99
2.6415-2.7473000.24462697X-RAY DIFFRACTION100
2.7473-2.87230.28332750.23582416X-RAY DIFFRACTION100
2.8723-3.02370.22892180.20742514X-RAY DIFFRACTION100
3.0237-3.213000.19172723X-RAY DIFFRACTION100
3.213-3.4610.22861950.17422538X-RAY DIFFRACTION100
3.461-3.80910.19252040.16082532X-RAY DIFFRACTION100
3.8091-4.3597000.15132746X-RAY DIFFRACTION100
4.3597-5.49060.17481300.15512643X-RAY DIFFRACTION100
5.4906-40.6220.19811980.19072644X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22880.02560.00251.61411.31493.506-0.1557-0.06110.0281-0.09140.15610.0902-0.20730.2338-00.2053-0.0565-0.02420.2288-0.01380.2156-55.704837.1466-12.4183
22.32740.67310.2072.0973-0.00783.2559-0.15870.20330.0242-0.12940.39150.0675-0.33650.3270.00030.2619-0.246-0.03640.33550.03950.2574-43.519756.79443.1263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 189
2X-RAY DIFFRACTION2chain BB9 - 191

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